package jalview.ext.forester.io;

import jalview.ext.archaeopteryx.JalviewBinding;
import jalview.ext.archaeopteryx.LoadedTreeAssociation;
import jalview.ext.archaeopteryx.ArchaeopteryxInit;
import jalview.ext.treeviewer.ExternalTreeParserI;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;

import java.io.File;
import java.io.IOException;

import org.forester.archaeopteryx.Archaeopteryx;
import org.forester.archaeopteryx.MainFrame;
import org.forester.util.ForesterUtil;

public class TreeParser implements ExternalTreeParserI<MainFrame>
{
  private final String filePath;

  private final File file;

  public TreeParser(final String treeFilePath)
  {
    final String possibleError = ForesterUtil.isReadableFile(treeFilePath);
    if (possibleError != null)
    {
      JvOptionPane.showMessageDialog(Desktop.desktop, possibleError,
              MessageManager.getString("label.problem_reading_tree_file"),
              JvOptionPane.WARNING_MESSAGE);

    }
    filePath = treeFilePath;
    file = new File(filePath);


  }

  public TreeParser(final File treeFile) throws IOException
  {
    final String possibleError = ForesterUtil.isReadableFile(treeFile);
    if (possibleError != null)
    {
      JvOptionPane.showMessageDialog(Desktop.desktop, possibleError,
              MessageManager.getString("label.problem_reading_tree_file"),
              JvOptionPane.WARNING_MESSAGE);

    }
    file = treeFile;
    filePath = file.getCanonicalPath();
  }

  @Override
  public MainFrame loadTree(AlignmentViewport viewport)
  {
    String[] AptxArgs = new String[] { "-c",
        "_aptx_jalview_configuration_file", filePath };
    MainFrame aptx = Archaeopteryx.main(AptxArgs);

    LoadedTreeAssociation bindAptxNodes = new LoadedTreeAssociation(
            viewport.getAlignment().getSequencesArray(),
            aptx.getMainPanel().getCurrentTreePanel().getPhylogeny());

    bindAptxNodes.associateLeavesToSequences();
    new JalviewBinding(aptx, viewport, bindAptxNodes.getAlignmentWithNodes(),
            bindAptxNodes.getNodesWithAlignment());

    ArchaeopteryxInit.bindFrameToJalview(aptx);

    return aptx;


  }

}